In this article, it is shown that available genetic tools for the omnipresent parasite Anguillicoloides crassus in European eels Anguilla anguilla are sensitive to different immigration rates into local A. anguilla stocks for two separated river systems. Relying on four highly polymorphic microsatellite markers, it was inferred that under natural recruitment, nematode samples meet Hardy–Weinberg expectations for a single panmictic population, while genetic signals show signs for a strong Wahlund effect most likely due to very recent population mixing under frequent restocking of young A. anguilla. This was indicated by a low but significant FST value among within-host populations (infrapopulations) along with high inbreeding indices FIS consistent over all loci. The latter signal is shown to stem from high levels of admixture and the presence of first-generation migrants, and alternative explanations such as marker- and sex-specific biases in the nematode populations could be dismissed. Moreover, the slightly increased degree of relatedness within infrapopulations in the stocked river system cannot explain the excessive inbreeding values found and are most likely a direct consequence of recent influx of already infected fish harbouring parasites with different genetic signatures. Applying a simulation approach using known variables from the nematode's invasion history, only the artificial introduction of a Wahlund effect leads to a close match between simulated and real data, which is a strong argument for using the parasite as a biological tag for detecting and characterizing fish translocation.